Results of a collaborative study of the EDNAP group regarding mitochondrial DNA heteroplasmy and segregation in hair shafts

Tully, Gillian; Barritt, Suzanne M.; Bender, Klaus; Brignon, E; Capelli, Cristian; Dimo-Simonin, N.; Eichmann, Cordula; Ernst, Claus; Lambert, C; Lareu, Marı́a Victoria; Ludes, Bertrand; Mevåg, B.; Parson, Walther; Pfeiffer, Heidi; Salas, Antonio; Schneider, P. M.; Staalstrom, E

doi:10.1016/s0379-0738(03)00181-6

Cited by 61 publications

(32 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Although having found several protocols for DNA extraction from hair shafts in the literature (for example, Higuchi et al, 1988;Schreiber et al, 1988;Wilson et al, 1995;Jehaes et al, 1998;Nozawa et al, 1999;Chang et al, 2002;Takayanagi et al, 2003;Wetton et al, 2003;Pfeiffer et al, 2004;Tully et al, 2004), we obtained our results using a method originally meant to extract DNA from feathers (Miyaki, 1996) rather than from hairs, upon which our improved protocol was based.…”

Section: Resultsmentioning

confidence: 92%

“…Some authors considered that DNA would be totally degraded during hair keratinization. Thus, it would not be possible to extract it from there, but this was proved wrong (Higuchi et al, 1988;Schreiber et al, 1988;Wilson et al, 1995;Jehaes et al, 1998;Nozawa et al, 1999;Takayanagi et al, 2003;Wetton et al, 2003;Tully et al, 2004;Pfeiffer et al, 2004). In the last years, DNA extraction from human hair shafts has been extensively used in forensics (Chang et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

DNA extraction from hair shafts of wild Brazilian felids and canids

Alberts

Ribeiro-Paes²,

Aranda-Selverio³

et al. 2010

Genet. Mol. Res.

View full text Add to dashboard Cite

ABSTRACT. Wild felids and canids are usually the main predators in the food chains where they dwell and are almost invisible to behavior and ecology researchers. Due to their grooming behavior, they tend to swallow shed hair, which shows up in the feces. DNA found in hair shafts can be used in molecular studies that can unravel, for instance, genetic variability, reproductive mode and family structure, and in some species, it is even possible to estimate migration and dispersion rates in given populations. First, however, DNA must be extracted from hair. We extracted successfully and dependably hair shaft DNA from eight wild Brazilian felids, ocelot, margay, oncilla, Geoffroy's cat, pampas cat, jaguarundi, puma, and jaguar, as well as the domestic cat and from three wild Brazilian canids, maned wolf, crab-eating fox, and hoary fox, as well as the domestic dog. Hair samples came mostly from feces collected at the São Paulo Zoo and were also gathered from non-sedated pet or from recently dead wild animals and were also collected from museum specimens. Fractions of hair samples were stained before DNA extraction, while most samples were not. Our extraction protocol is based on a feather DNA extraction technique, based in the phenol:chloroform:isoamyl alcohol general method, with proteinase K as digestive enzyme.

show abstract

Section: Resultsmentioning

confidence: 92%

Section: Introductionmentioning

confidence: 99%

DNA extraction from hair shafts of wild Brazilian felids and canids

Alberts

Ribeiro-Paes²,

Aranda-Selverio³

et al. 2010

Genet. Mol. Res.

View full text Add to dashboard Cite

show abstract

“…It seems that a Electrophoresis 2005, 26, 3414-3429 nonoptimized sequencing setup can induce an elevated level of phantom mutations. Most phantom mutations so far have been pinpointed in analyses of hypervariable segments I and II (HVS-I and HVS-II)-simply because these parts of the control region (CR) were most popular in large-scale mtDNA sequencing efforts of anthropology and forensics [2][3][4]. The coding region, mainly targeted in medical studies, is, however, not exempt of such problems [5].…”

Section: Introductionmentioning

confidence: 99%

“…Among the approaches to DNA sequencing, cycle sequencing with dye terminators is most commonly used, followed by cycle sequencing with dye primers or dRhodamine terminators [2,4,20]. Especially for cycle sequencing with dye terminators, a variety of sequencing chemistry versions are commercially available (AB, Applied Biosystems, Foster City, CA, USA).…”

Section: Introductionmentioning

confidence: 99%

Phantom mutation hotspots in human mitochondrial DNA

Brandstätter¹,

Sänger²,

Lutz-Bonengel³

et al. 2005

Electrophoresis

View full text Add to dashboard Cite

Phantom mutations are systematic artifacts generated in the course of the sequencing process. Contra common belief these artificial mutations are nearly ubiquitous in sequencing results, albeit at frequencies that may vary dramatically. The amount of artifacts depends not only on the sort of automated sequencer and sequencing chemistry employed, but also on other lab-specific factors. An experimental study executed on four samples under various combinations of sequencing conditions revealed a number of phantom mutations occurring at the same sites of mitochondrial DNA (mtDNA) repeatedly. To confirm these and identify further hotspots for artifacts, > 5000 mtDNA electropherograms were screened for artificial patterns. Further, > 30 000 published hypervariable segment I sequences were compared at potential hotspots for phantom mutations, especially for variation at positions 16085 and 16197. Resequencing of several samples confirmed the artificial nature of these and other polymorphisms in the original publications. Single-strand sequencing, as typically executed in medical and anthropological studies, is thus highly vulnerable to this kind of artifacts. In particular, phantom mutation hotspots could easily lead to misidentification of somatic mutations and to misinterpretations in all kinds of clinical mtDNA studies.

show abstract

“…Forster et al (2002) observed that radiationassociated point mutations are evolutionary hotspots in the mtDNA genome. The model includes: (1) somatic differences between tissues of the same individual, including situations of forensic interest, where there are differences between fragments of the same hair-shaft (Salas et al, 2001;Tully et al, 2003), (2) intergenerational mutations between mother and offspring, and (3) the generation of heteroplasmy in normal cells (Stoneking 2000). In addition, this model would explain the lack of association between nMI (and malignancy) and mtDNA instability.…”

mentioning

confidence: 99%

mtDNA mutations in tumors of the central nervous system reflect the neutral evolution of mtDNA in populations

et al. 2003

View full text Add to dashboard Cite

Mitochondrial DNA (mtDNA) instability has been observed in different types of cancer, including colorectal, breast, and gastric cancer. The relationship between the occurrence of such alteration and the nuclear microsatellite instability (nMI) status of the neoplastic cells remains controversial. In an attempt to clarify this issue, we sequenced the first and second mtDNA hypervariable regions, and typed the mitochondrial (CA) n dinucleotide polymorphism in 69 patients with primary tumors of the central nervous system (CNS), previously screened for nMI. Tumor samples showed 27 D-loop sequence changes (39.1%) compared to the corresponding blood samples. Microsatellite homoplasmic allele mutations were detected in four cases (5.8%). We did not find significant associations of the mtDNA instability status with clinicopathological parameters including sex, age, tumor size, and duration of clinical course. Neither did we find any association between mtDNA and nuclear instabilities, indicating that, at least in CNS tumors, they respond to different DNA repair mechanisms. We have also compiled the mtDNA instabilities previously reported by other authors for several types of tumors, comparing them to mtDNA polymorphisms in human populations. Most of the tumor-associated changes are common human polymorphisms and mutational hotspots. To explain the molecular behavior of mtDNA instability in tumors, we propose a model also common to other biological situations.

show abstract

Results of a collaborative study of the EDNAP group regarding mitochondrial DNA heteroplasmy and segregation in hair shafts

Cited by 61 publications

References 28 publications

DNA extraction from hair shafts of wild Brazilian felids and canids

DNA extraction from hair shafts of wild Brazilian felids and canids

Phantom mutation hotspots in human mitochondrial DNA

mtDNA mutations in tumors of the central nervous system reflect the neutral evolution of mtDNA in populations

Contact Info

Product

Resources

About